My theory is that either A. They did load a virus or trojan of some kind on that server for tracking purposes (although i don't see how useful it would be seeing as how the entire system is supposedly encrypted.

Or B they brought it back and someone was like, why do we have this? We should not have taken this. Get it back there now!. And therefore it would be a mistake, of which the FBI never admits to their mistakes.

So if they came and went as they pleased they had physical access to the entire data center without any escorts? Seems odd that a motion sensor was triggered one time. No other workers in the facility? If it was your data center wouldn't you be all over these guys and probably not even let them hook it back up themselves?

What if hooking it up was merely the payload and it infected something else and removed itself from the original host device...

They wouldn't even need to have done a total wipe. Cosidering that a wifi adapter can be crammed onto an SD card (Eyefi) for a consumer level device, there could be an incredibly hard to detect peice of hardware installed somewhere passively monitoring and broadcasting to other equipment in the same colo.